Yup. There aren’t any antidiscrimination laws in Japan, so establishments are allowed to say “Japanese only.” For the most part, you don’t run into this on a daily basis, but there are some notable exceptions.
For the most part, Japanese don’t despise foreigners, but there are exceptions to the welcome wagon. Probably the biggest problem is renting apartments. That’s the first time I was ever clearly discriminated against. When my (now ex-)wife and I were looking for a place, she would go to the real estate agent first and get the OK, but when I showed up, suddenly every damn place was gone.
We walked into one agent’s office and asked about one of the apartments advertised in the window. Nope, it had be rented out that morning, and amazingly enough, he knew that without calling the listed agent. Same for all other places. I asked him why he was still advertising it when it was gone and he took pulled the paper off the window. I thoughtfully ripped it up into shreds for him and threw it away, along will every other already rented place.
I used to go out with a lady who lived off the income from a few apartments. She would hang out in Roppongi, the bar district where the gaijin (foreigners, especially whites) and was hoping to meet and marry a Western guy. The funny thing is that she wouldn’t rent to foreigners. She’d fuck them, but not rent to them, go figure.
That said, for the most part the outright discrimination shown in the cited site falls under two categories. The first are (mostly) Japanese style baths and similar establishments in Hokkaido, the northern island, where there are problems with Russian sailors. Many of the cited signs are in Russian. Apparently some normal establishments also discriminate against Russians, but I haven’t been there myself.
The second place where Japanese Only is frequently seen would be in the mizushoubai (lit. water business, various “night establishments” eg. Seedy businesses.) Japanese have their own quirks when it comes to mizushoubai, which for the most part involve charging far too much for less service than would be expected by reputable US governors.
This may be a language issue. Lacking the ability to explain to the more-often-than-not less-than-sober foreign customers that they can get a hand job, but absolutely nothing more, they simply say “No foreigners.” Or, if it’s a hostess club, no one has the ability to adequately tell the poor saps that regardless of the hundreds of dollars they just dropped, they’re not allowed to touch at all.
I was never into either of those scenes, but I’ve had a number of friends who have been kept out of these types of places. One friend remarked on the irony of once place which employed Philippine hostesses but still rejected foreign customers.